I had the same problem on my 96 mustang, except mine blew the eec fuse every time. My problem was the harness grounding itself out on the egr tube that runs up close to the firewall
Dont know if that would help u any but if u gave us more detail in wat the car is specifically doin im sure one of is may pinpoint the problem and help u fix it.
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Oh and a tune is kinda like remappin the computer when u add any mods to it i.e. intake long tubes etc
1996 Mustang GT, 17x9 front and 17x10.5 cobra r replica rims, 255/40/17 front 285/40/17 rear at the moment,
o/r x-pipe flow master 40 series dump downs, cai/ram intake, 75mm c&l throttle body and plenum, pi heads and intake swap, msd wires, stock gears, untuned at the moment, no dyno numbers for now.